miRge3 reference library not available in the server

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1

Admins, please fix the following issue

I’m trying to use the miRge3 pipeline for miRNA seq analyses (done using the MGI platform), the miRge3 human library is not available (nor can it be manually uploaded)

2

Welcome @nive3437

Yes, the tool is newly available at the UseGalaxy.eu server (only so far) and it seems to not have any of the tool’s native indexes loaded yet. We can make a request.

This was a good question! Let’s see what the developers think! :slight_smile:

3

This is what is displayed

"Parameter ‘organism_name’: an invalid option (None) was selected, please verify

Reference Library * required

No options available."-

Pre-installed miRge3 reference library for your organism"

I request that developers fix this as soon as possible, as it would help me analyze my data in one go. Thank you.

4

Hi @nive3437
Thanks for using Galaxy and putting forward this issue!

We have installed the human and mouse reference data. Please run the tool again and let us know if you encounter any further issues.

Best,

Pavan

5

Update: I ran some tests and think this still needs a bit of adjustment, but I’m curious what happens with you too @nive3437 ! Fwiw, you have some trouble getting the Run Tool button to activate, please see the original issue ticket for what I reported and the workaround.

6

Thank you for your quick response. The following error is encountered.

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7

Thanks for the quick response. the following error occurred after running.

8

ii tried running the tool with one fast.q (gz) file- gave no cut off, still found this error Fatal error:

Tool generated the following standard error:

        /usr/local/lib/python3.10/site-packages/Bio/pairwise2.py:278: BiopythonDeprecationWarning: Bio.pairwise2 has been deprecated, and we intend to remove it in a future release of Biopython. As an alternative, please consider using Bio.Align.PairwiseAligner as a replacement, and contact the Biopython developers if you still need the Bio.pairwise2 module.

warnings.warn(

9

Thanks @nive3437! Your results help to confirm the open issue.

It looks like @pavanvidem is working on this a bit more to tune things up! Let’s watch for the update. → Request: miRge3 reference data status · Issue #2394 · usegalaxy-eu/infrastructure-playbook · GitHub